For any other Linux 64bit users out there, you can download a 64bit version of ioquake3 - with bot support - here: lvlworld.com/lvl/ioquake3_64bit.zip

This was compiled for Linux Mint 17 (by me) from the current trunk version of ioquake3 and includes a dedicated server as well as the standard client.

There is a good chance it will work with any other Linux 64 bit version.

For some reason the version that came with Linux Mint 16 worked for me (using the Software Manager). It is possible this was the 32bit version which does not have the same issue with bots.

The version of ioquake3 with Mint 17 does work, but it has no bot support - so I compiled my own version and everything (so far) works without an issue.